Hello and Alingers for Transcriptome analysis?

[s.amberkar]

Dear All,

Just wanted to say a big Hello and thanks to the community which has served its purpose well for so long. If it hadn't been for this community, I wouldn't have learned the basic things of genomics before jumping on to the more specialised articles.
I'm currently working on establishing a RNA-seq analysis using bcbio; my main issue being selection of an aligner. I have been looking into STAR, HISAT2 (successor of Bowtie,Bowtie2), SNAPR, Rsubread and TopHat. Currently, there aren't any analysis-specific requirements.
Any thoughts?

Cheers,
Sandeep

[Brian Bushnell]

I would toss BBMap in as another possibility; it's more robust against low-quality data and polymorphisms, as compared to other RNA-seq aligners.

[gringer]

There's Kallisto as well, which is stupidly fast and claims to be able to do isoform-level count estimation.